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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 6.3.2.4

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Search Summary

This query matches 63 Structures.

Refinements

Structure Determination Methodology

experimental (63)

Scientific Name of Source Organism

	Thermus thermophilus HB8 (12)
	Pseudomonas aeruginosa PAO1 (5)
	Yersinia pestis (5)
	Escherichia coli (3)
	Escherichia coli K-12 (3)
	Staphylococcus aureus (3)
	Thermus thermophilus (3)
	Xanthomonas oryzae pv. oryzae KACC 10331 (3)
	Acinetobacter baumannii ACICU (2)
	Salmonella enterica subsp. enterica serovar Typhimurium (2)

More...

Taxonomy

	Bacteria (63)
	other sequences (1)

Experimental Method

X-RAY DIFFRACTION (63)

Polymer Entity Type

Protein (63)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (14)
	2.0 - 2.5 (40)
	2.5 - 3.0 (6)

Release Date

	1995 - 1999 (3)
	2000 - 2004 (1)
	2005 - 2009 (12)
	2010 - 2014 (16)
	2015 - 2019 (13)
	2020 - 2024 (18)

Enzyme Classification Name

Ligases (63)

Symmetry Type

	Cyclic (57)
	Asymmetric (8)

SCOP Classification

	Alpha and beta proteins (a/b) (54)
	Alpha and beta proteins (a+b) (54)
	Artifacts (17)

AllSelected

1 to 25 of 63 Structures

Page 1 of 3

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1EHI \| pdb_00001ehi	Download File View File

D-ALANINE:D-LACTATE LIGASE (LMDDL2) OF VANCOMYCIN-RESISTANT LEUCONOSTOC MESENTEROIDES

Kuzin, A.P., Sun, T., Jorczak-Baillass, J., Healy, V.L., Walsh, C.T., Knox, J.R.

(2000) Structure 8: 463-470

Released	2000-05-23
Method	X-RAY DIFFRACTION 2.38 Å
Organisms	Leuconostoc mesenteroides
Macromolecule	D-ALANINE:D-LACTATE LIGASE (protein)
Unique Ligands	ADP, MG, PHY

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1IOV \| pdb_00001iov	Download File View File

COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE

Knox, J.R., Moews, P.C., Fan, C.

(1997) Biochemistry 36: 2531-2538

Released	1997-02-12
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Escherichia coli
Macromolecule	D-ALA\:D-ALA LIGASE (protein)
Unique Ligands	ADP, MG, POB

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1IOW \| pdb_00001iow	Download File View File

COMPLEX OF Y216F D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHINATE

Knox, J.R., Moews, P.C., Fan, C.

(1997) Biochemistry 36: 2531-2538

Released	1997-02-12
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Escherichia coli
Macromolecule	D-ALA\:D-ALA LIGASE (protein)
Unique Ligands	ADP, MG, PHY

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2DLN \| pdb_00002dln	Download File View File

VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS RESOLUTION

Knox, J.R., Moews, P.C., Fan, C.

(1994) Science 266: 439-443

Released	1995-11-01
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Escherichia coli
Macromolecule	D-ALANINE--D-ALANINE LIGASE (protein)
Unique Ligands	ADP, MG, PHY

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2FB9 \| pdb_00002fb9	Download File View File

Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes

Lee, J.H., Na, Y., Eom, S.H.

(2006) Proteins 64: 1078-1082

Released	2006-08-29
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus caldophilus
Macromolecule	D-alanine:D-alanine ligase (protein)

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2I80 \| pdb_00002i80	Download File View File

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies

Liu, S., Chang, J.S., Herberg, J.T., Horng, M.-M., Tomich, P.K., Lin, A.H., Marotti, K.R.

(2006) Proc Natl Acad Sci U S A 103: 15178-15183

Released	2006-09-26
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Staphylococcus aureus
Macromolecule	D-alanine-D-alanine ligase (protein)
Unique Ligands	G1L

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2I87 \| pdb_00002i87	Download File View File

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies

Liu, S., Chang, J.S., Herberg, J.T., Horng, M., Tomich, P.K., Lin, A.H., Marotti, K.R.

(2006) Proc Natl Acad Sci U S A 103: 15178-15183

Released	2006-10-03
Method	X-RAY DIFFRACTION 2 Å
Organisms	Staphylococcus aureus subsp. aureus COL
Macromolecule	D-alanine-D-alanine ligase (protein)
Unique Ligands	SO4

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2I8C \| pdb_00002i8c	Download File View File

Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies

Liu, S., Chang, J.S., Herberg, J.T., Horng, M., Tomich, P.K., Lin, A.H., Marotti, K.R.

(2006) Proc Natl Acad Sci U S A 103: 15178-15183

Released	2006-09-26
Method	X-RAY DIFFRACTION 2.46 Å
Organisms	Staphylococcus aureus subsp. aureus COL
Macromolecule	D-alanine-D-alanine ligase (protein)
Unique Ligands	ADP, MG, SO4

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2PVP \| pdb_00002pvp	Download File View File

Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori

Wu, D., Zhang, L., Jiang, H., Shen, X.

(2008) Proteins 72: 1148-1160

Released	2008-04-01
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Helicobacter pylori SS1
Macromolecule	D-alanine-D-alanine ligase (protein)

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2YZG \| pdb_00002yzg	Download File View File

Crystal structure of D-ALA:D-ALA Ligase from Thermus thermophilus HB8

Kitamura, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-11-06
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermus thermophilus HB8
Macromolecule	D-alanine--D-alanine ligase (protein)

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2YZM \| pdb_00002yzm	Download File View File

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

Kitamura, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-11-06
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Thermus thermophilus HB8
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	DAL

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2YZN \| pdb_00002yzn	Download File View File

Crystal structure of D-alanine:D-Alanine Ligase with AMPPNP from Thermus thermophilus HB8.

Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2007-11-06
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermus thermophilus HB8
Macromolecule	D-alanine-D-alanine ligase (protein)
Unique Ligands	ANP

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2ZDG \| pdb_00002zdg	Download File View File

Crystal structure of D-Alanine:D-Alanine Ligase with ADP from Thermus thermophius HB8

Kitamura, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-05-27
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Thermus thermophilus
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	ADP, MG

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2ZDH \| pdb_00002zdh	Download File View File

Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8

Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-05-27
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Thermus thermophilus
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	ADP, DAL, MG

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2ZDQ \| pdb_00002zdq	Download File View File

Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus thermophius HB8

Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

To be published

Released	2008-05-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Thermus thermophilus
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	ATP, DAL

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3I12 \| pdb_00003i12	Download File View File

The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Zhang, R., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2009-08-18
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	D-alanine-D-alanine ligase A (protein)
Unique Ligands	ADP

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3K3P \| pdb_00003k3p	Download File View File

Crystal Structure of the Apo Form of D-Alanine:D-Alanine Ligase (DDl) from Streptococcus mutans

Lu, Y.

(2010) Protein Pept Lett 17: 1053-1057

Released	2010-09-15
Method	X-RAY DIFFRACTION 2.23 Å
Organisms	Streptococcus mutans
Macromolecule	D-alanine--D-alanine ligase (protein)

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3LWB \| pdb_00003lwb	Download File View File

Crystal Structure of apo D-alanine:D-alanine Ligase (Ddl) from Mycobacterium tuberculosis

Bruning, J.B., Murillo, A.C., Chacon, O., Barletta, R.G., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

(2011) Antimicrob Agents Chemother 55: 291-301

Released	2010-03-09
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Mycobacterium tuberculosis
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	NO3

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3N8D \| pdb_00003n8d	Download File View File

Crystal structure of Staphylococcus aureus VRSA-9 D-Ala:D-Ala ligase

Saul, F.A., Haouz, A., Meziane-Cherif, D.

(2010) J Bacteriol 192: 5465-5471

Released	2010-10-13
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Staphylococcus aureus
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	ANP, CL, SO4

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3Q1K \| pdb_00003q1k	Download File View File

The Crystal Structure of the D-alanyl-alanine Synthetase A from Salmonella enterica Typhimurium Complexed with ADP

Zhang, R., Maltseva, N., Papazisi, L., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2011-01-12
Method	X-RAY DIFFRACTION 2.202 Å
Organisms	Salmonella enterica subsp. enterica serovar Typhimurium
Macromolecule	D-alanine--D-alanine ligase A (protein)
Unique Ligands	ADP, FMT, GOL, MG, SO4

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3R23 \| pdb_00003r23	Download File View File

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis

Kim, Y., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2011-03-30
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Bacillus anthracis str. Ames
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	EDO

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3R5F \| pdb_00003r5f	Download File View File

Crystal structure of D-alanine-D-alnine ligase from Xanthomonas oryzae pv. oryzae with ATP

Doan, T.T.N., Kim, J.K., Kang, L.W.

To be published

Released	2011-05-25
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Xanthomonas oryzae pv. oryzae KACC 10331
Macromolecule	D-alanine--D-alanine ligase 1 (protein)
Unique Ligands	ATP, MG

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3R5X \| pdb_00003r5x	Download File View File

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

Kim, Y., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published

Released	2011-04-06
Method	X-RAY DIFFRACTION 2 Å
Organisms	Bacillus anthracis
Macromolecule	D-alanine--D-alanine ligase (protein)
Unique Ligands	ACY, ATP, CA, EDO, MG

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3RFC \| pdb_00003rfc	Download File View File

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

Doan, T.T.N., Kim, J.K., Ahn, Y.J., Kang, L.W.

To be published

Released	2011-05-04
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Xanthomonas oryzae pv. oryzae MAFF 311018
Macromolecule	D-alanine--D-alanine ligase 1 (protein)
Unique Ligands	ADP, MG